Align ABC transporter permease (characterized, see rationale)
to candidate Pf1N1B4_3217 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3217 Length = 307 Score = 247 bits (631), Expect = 2e-70 Identities = 140/303 (46%), Positives = 197/303 (65%), Gaps = 17/303 (5%) Query: 6 QQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAP 65 QQ++NGL +GS YALIA+GYTMVYGII +INFAHGEV MIG+ ++ I + AM G Sbjct: 9 QQLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL--AMLGLD 66 Query: 66 GWVILLLATIIAC-VVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWK 124 +L+ A +A VV + + IE++AYRPLR S RL PLI+AIGMSI LQ ++ Sbjct: 67 SVPLLMTAAFLATIVVTSAYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLAQD 126 Query: 125 PNYKPYPTMLPSSPFEIG--GA---FITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 K ++P + F IG GA I+ QI++ VT VA+ L ++ + LGRA RA Sbjct: 127 SKDKSISNLIPGN-FAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRA 185 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 AE+ ++A+L+G+ + +I+ TF+IGA LAAIA ++ + YG GFL GLKAFTAA Sbjct: 186 CAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTAA 245 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299 V GGIG++ GA++GG++LG+ EA G+ + G Y D+ AF +L+++L RP+G Sbjct: 246 VLGGIGSIPGAMLGGLVLGVAEAFGA--------DIFGDQYKDVVAFGLLVLVLLFRPTG 297 Query: 300 LLG 302 LLG Sbjct: 298 LLG 300 Lambda K H 0.327 0.142 0.419 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 265 Number of extensions: 12 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 309 Length of database: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory